Hello,
I'm having an odd problem after updating to the latest version of Galaxy. My users prepare data for analysis using data manager tools, such as "data_manager_bwa_mem_index_builder". When an attempt is made to run one of these tools, a pop up window opens stating "Tool request failed" and underneath "Uncaught error". I've pored over all the Galaxy system logs and can't find anything that might indicate what is happening. I've uninstalled and reinstalled the data manager tools, restarted both the Galaxy service and the server, to no avail. I get this same error with any installed data manager, yet all the standard tools are executing correctly and don't seem to be having any issues.
If anyone can offer some insight or suggestions for resolving this issue, I'd be most appreciative.
Best regards,
Hi Scott,
I've recently hit the exact same problem. Have you had any success since then with resolving this? I did some poking around and made a bit of progress, but still no solution.
The Data Manager page under Run Data Manager Tools contains URLs like this:
https://galaxy.example.com/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdev...
Loading that URL results in an attempted load of:
https://galaxy.example.com/api/tools/toolshed.g2.bx.psu.edu%2Frepos%2Fdevtea... ?
Which results in a 404 error. I believe the escaping of the slashes is accidental, as the they are in the path and not in parameters. Changing the %2F to / as shown here:
https://galaxy.example.com/api/tools/toolshed.g2.bx.psu.edu/repos/devteam/da... ?
results in the URL being found and you get back a bunch of JSON about the tool. I tried looking in the Galaxy code to see if I could quickly determine where the /root controller is, but I wasn't successful. Perhaps this is now enough information that one of the developers might be able to help us.
-Will
On Mon, Apr 11, 2016 at 9:55 AM, Scott Szakonyi Scott.B.Szakonyi.1@nd.edu wrote:
Hello,
I'm having an odd problem after updating to the latest version of Galaxy. My users prepare data for analysis using data manager tools, such as "data_manager_bwa_mem_index_builder". When an attempt is made to run one of these tools, a pop up window opens stating "Tool request failed" and underneath "Uncaught error". I've pored over all the Galaxy system logs and can't find anything that might indicate what is happening. I've uninstalled and reinstalled the data manager tools, restarted both the Galaxy service and the server, to no avail. I get this same error with any installed data manager, yet all the standard tools are executing correctly and don't seem to be having any issues.
If anyone can offer some insight or suggestions for resolving this issue, I'd be most appreciative.
Best regards,
-- Scott B. Szakonyi Research Programmer
*Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi Will,
We did manage to solve that problem by changing the Apache configuration. We added "AllowEncodedSlashes On" to httpd.conf. I'm not sure why the URL encoding changed, only that it did. See if that helps you.
Best,
Scott
On Tue, May 10, 2016 at 8:17 PM, Will Holtz wholtz@lygos.com wrote:
Hi Scott,
I've recently hit the exact same problem. Have you had any success since then with resolving this? I did some poking around and made a bit of progress, but still no solution.
The Data Manager page under Run Data Manager Tools contains URLs like this:
https://galaxy.example.com/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdev...
Loading that URL results in an attempted load of:
https://galaxy.example.com/api/tools/toolshed.g2.bx.psu.edu%2Frepos%2Fdevtea... ?
Which results in a 404 error. I believe the escaping of the slashes is accidental, as the they are in the path and not in parameters. Changing the %2F to / as shown here:
https://galaxy.example.com/api/tools/toolshed.g2.bx.psu.edu/repos/devteam/da... ?
results in the URL being found and you get back a bunch of JSON about the tool. I tried looking in the Galaxy code to see if I could quickly determine where the /root controller is, but I wasn't successful. Perhaps this is now enough information that one of the developers might be able to help us.
-Will
On Mon, Apr 11, 2016 at 9:55 AM, Scott Szakonyi <Scott.B.Szakonyi.1@nd.edu
wrote:
Hello,
I'm having an odd problem after updating to the latest version of Galaxy. My users prepare data for analysis using data manager tools, such as "data_manager_bwa_mem_index_builder". When an attempt is made to run one of these tools, a pop up window opens stating "Tool request failed" and underneath "Uncaught error". I've pored over all the Galaxy system logs and can't find anything that might indicate what is happening. I've uninstalled and reinstalled the data manager tools, restarted both the Galaxy service and the server, to no avail. I get this same error with any installed data manager, yet all the standard tools are executing correctly and don't seem to be having any issues.
If anyone can offer some insight or suggestions for resolving this issue, I'd be most appreciative.
Best regards,
-- Scott B. Szakonyi Research Programmer
*Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- The information contained in this e-mail message or any attachment(s) may be confidential and/or privileged and is intended for use only by the individual(s) to whom this message is addressed. If you are not the intended recipient, any dissemination, distribution, copying, or use is strictly prohibited. If you receive this e-mail message in error, please e-mail the sender at wholtz@lygos.com and destroy this message and remove the transmission from all computer directories (including e-mail servers).
Please consider the environment before printing this email.
Hello Scott,
Thanks for the helpful reply! Adding"AllowEncodedSlashes On" did allow me to access the Data Manager tools. However, the Apache documentation has the following note, "If encoded slashes are needed in path info, use of NoDecode is strongly recommended as a security measure. Allowing slashes to be decoded could potentially allow unsafe paths." So this probably isn't a good long-term solution.
thanks, -Will
On Wed, May 11, 2016 at 9:03 AM, Scott Szakonyi Scott.B.Szakonyi.1@nd.edu wrote:
Hi Will,
We did manage to solve that problem by changing the Apache configuration. We added "AllowEncodedSlashes On" to httpd.conf. I'm not sure why the URL encoding changed, only that it did. See if that helps you.
Best,
Scott
On Tue, May 10, 2016 at 8:17 PM, Will Holtz wholtz@lygos.com wrote:
Hi Scott,
I've recently hit the exact same problem. Have you had any success since then with resolving this? I did some poking around and made a bit of progress, but still no solution.
The Data Manager page under Run Data Manager Tools contains URLs like this:
https://galaxy.example.com/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdev...
Loading that URL results in an attempted load of:
https://galaxy.example.com/api/tools/toolshed.g2.bx.psu.edu%2Frepos%2Fdevtea... ?
Which results in a 404 error. I believe the escaping of the slashes is accidental, as the they are in the path and not in parameters. Changing the %2F to / as shown here:
https://galaxy.example.com/api/tools/toolshed.g2.bx.psu.edu/repos/devteam/da... ?
results in the URL being found and you get back a bunch of JSON about the tool. I tried looking in the Galaxy code to see if I could quickly determine where the /root controller is, but I wasn't successful. Perhaps this is now enough information that one of the developers might be able to help us.
-Will
On Mon, Apr 11, 2016 at 9:55 AM, Scott Szakonyi < Scott.B.Szakonyi.1@nd.edu> wrote:
Hello,
I'm having an odd problem after updating to the latest version of Galaxy. My users prepare data for analysis using data manager tools, such as "data_manager_bwa_mem_index_builder". When an attempt is made to run one of these tools, a pop up window opens stating "Tool request failed" and underneath "Uncaught error". I've pored over all the Galaxy system logs and can't find anything that might indicate what is happening. I've uninstalled and reinstalled the data manager tools, restarted both the Galaxy service and the server, to no avail. I get this same error with any installed data manager, yet all the standard tools are executing correctly and don't seem to be having any issues.
If anyone can offer some insight or suggestions for resolving this issue, I'd be most appreciative.
Best regards,
-- Scott B. Szakonyi Research Programmer
*Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- The information contained in this e-mail message or any attachment(s) may be confidential and/or privileged and is intended for use only by the individual(s) to whom this message is addressed. If you are not the intended recipient, any dissemination, distribution, copying, or use is strictly prohibited. If you receive this e-mail message in error, please e-mail the sender at wholtz@lygos.com and destroy this message and remove the transmission from all computer directories (including e-mail servers).
Please consider the environment before printing this email.
-- Scott B. Szakonyi Research Programmer
*Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu
Will, Scott,
You should be able to use the NoDecode flag on the AllowEncodedSlashes option without any problems. Galaxy will have decoded the slashes internally by the time the request has reached the controller, and the tool in question will be found.
- Dave Bouvier http://galaxyproject.org http://usegalaxy.org
On 05/11/2016 12:12 PM, Will Holtz wrote:
Hello Scott,
Thanks for the helpful reply! Adding"AllowEncodedSlashes On" did allow me to access the Data Manager tools. However, the Apache documentation has the following note, "If encoded slashes are needed in path info, use of NoDecode is strongly recommended as a security measure. Allowing slashes to be decoded could potentially allow unsafe paths." So this probably isn't a good long-term solution.
thanks, -Will
On Wed, May 11, 2016 at 9:03 AM, Scott Szakonyi <Scott.B.Szakonyi.1@nd.edu mailto:Scott.B.Szakonyi.1@nd.edu> wrote:
Hi Will, We did manage to solve that problem by changing the Apache configuration. We added "AllowEncodedSlashes On" to httpd.conf. I'm not sure why the URL encoding changed, only that it did. See if that helps you. Best, Scott On Tue, May 10, 2016 at 8:17 PM, Will Holtz <wholtz@lygos.com <mailto:wholtz@lygos.com>> wrote: Hi Scott, I've recently hit the exact same problem. Have you had any success since then with resolving this? I did some poking around and made a bit of progress, but still no solution. The Data Manager page under Run Data Manager Tools contains URLs like this: https://galaxy.example.com/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_dbkeys_all_fasta%2Fdata_manager_fetch_genome_all_fasta_dbkey%2F0.0.1 Loading that URL results in an attempted load of: https://galaxy.example.com/api/tools/toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_dbkeys_all_fasta%2Fdata_manager_fetch_genome_all_fasta_dbkey%2F0.0.1/build? Which results in a 404 error. I believe the escaping of the slashes is accidental, as the they are in the path and not in parameters. Changing the %2F to / as shown here: https://galaxy.example.com/api/tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/data_manager_fetch_genome_all_fasta_dbkey/0.0.1/build? results in the URL being found and you get back a bunch of JSON about the tool. I tried looking in the Galaxy code to see if I could quickly determine where the /root controller is, but I wasn't successful. Perhaps this is now enough information that one of the developers might be able to help us. -Will On Mon, Apr 11, 2016 at 9:55 AM, Scott Szakonyi <Scott.B.Szakonyi.1@nd.edu <mailto:Scott.B.Szakonyi.1@nd.edu>> wrote: Hello, I'm having an odd problem after updating to the latest version of Galaxy. My users prepare data for analysis using data manager tools, such as "data_manager_bwa_mem_index_builder". When an attempt is made to run one of these tools, a pop up window opens stating "Tool request failed" and underneath "Uncaught error". I've pored over all the Galaxy system logs and can't find anything that might indicate what is happening. I've uninstalled and reinstalled the data manager tools, restarted both the Galaxy service and the server, to no avail. I get this same error with any installed data manager, yet all the standard tools are executing correctly and don't seem to be having any issues. If anyone can offer some insight or suggestions for resolving this issue, I'd be most appreciative. Best regards, -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu <http://crc.nd.edu/> ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- The information contained in this e-mail message or any attachment(s) may be confidential and/or privileged and is intended for use only by the individual(s) to whom this message is addressed. If you are not the intended recipient, any dissemination, distribution, copying, or use is strictly prohibited. If you receive this e-mail message in error, please e-mail the sender at wholtz@lygos.com <mailto:wholtz@lygos.com> and destroy this message and remove the transmission from all computer directories (including e-mail servers). Please consider the environment before printing this email. -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu <http://crc.nd.edu/>-- The information contained in this e-mail message or any attachment(s) may be confidential and/or privileged and is intended for use only by the individual(s) to whom this message is addressed. If you are not the intended recipient, any dissemination, distribution, copying, or use is strictly prohibited. If you receive this e-mail message in error, please e-mail the sender at wholtz@lygos.com mailto:wholtz@lygos.com and destroy this message and remove the transmission from all computer directories (including e-mail servers).
Please consider the environment before printing this email.
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi Dave,
The NoDecode flag did work for me. I added a note to the apache configuration page of the galaxy wiki: https://wiki.galaxyproject.org/Admin/Config/ApacheProxy
Thanks!
-Will
On Wed, May 11, 2016 at 10:23 AM, Dave Bouvier dave@bx.psu.edu wrote:
Will, Scott,
You should be able to use the NoDecode flag on the AllowEncodedSlashes option without any problems. Galaxy will have decoded the slashes internally by the time the request has reached the controller, and the tool in question will be found.
Dave Bouvier http://galaxyproject.org http://usegalaxy.org
On 05/11/2016 12:12 PM, Will Holtz wrote:
Hello Scott,
Thanks for the helpful reply! Adding"AllowEncodedSlashes On" did allow me to access the Data Manager tools. However, the Apache documentation has the following note, "If encoded slashes are needed in path info, use of NoDecode is strongly recommended as a security measure. Allowing slashes to be decoded could potentially allow unsafe paths." So this probably isn't a good long-term solution.
thanks, -Will
On Wed, May 11, 2016 at 9:03 AM, Scott Szakonyi <Scott.B.Szakonyi.1@nd.edu mailto:Scott.B.Szakonyi.1@nd.edu> wrote:
Hi Will, We did manage to solve that problem by changing the Apache configuration. We added "AllowEncodedSlashes On" to httpd.conf. I'm not sure why the URL encoding changed, only that it did. See if that helps you. Best, Scott On Tue, May 10, 2016 at 8:17 PM, Will Holtz <wholtz@lygos.com <mailto:wholtz@lygos.com>> wrote: Hi Scott, I've recently hit the exact same problem. Have you had any success since then with resolving this? I did some poking around and made a bit of progress, but still no solution. The Data Manager page under Run Data Manager Tools contains URLs like this:https://galaxy.example.com/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdev...
Loading that URL results in an attempted load of:https://galaxy.example.com/api/tools/toolshed.g2.bx.psu.edu%2Frepos%2Fdevtea... ?
Which results in a 404 error. I believe the escaping of the slashes is accidental, as the they are in the path and not in parameters. Changing the %2F to / as shown here:https://galaxy.example.com/api/tools/toolshed.g2.bx.psu.edu/repos/devteam/da... ?
results in the URL being found and you get back a bunch of JSON about the tool. I tried looking in the Galaxy code to see if I could quickly determine where the /root controller is, but I wasn't successful. Perhaps this is now enough information that one of the developers might be able to help us. -Will On Mon, Apr 11, 2016 at 9:55 AM, Scott Szakonyi <Scott.B.Szakonyi.1@nd.edu <mailto:Scott.B.Szakonyi.1@nd.edu>> wrote: Hello, I'm having an odd problem after updating to the latest version of Galaxy. My users prepare data for analysis using data manager tools, such as "data_manager_bwa_mem_index_builder". When an attempt is made to run one of these tools, a pop up window opens stating "Tool request failed" and underneath "Uncaught error". I've pored over all the Galaxy system logs and can't find anything that might indicate what is happening. I've uninstalled and reinstalled the data manager tools, restarted both the Galaxy service and the server, to no avail. I get this same error with any installed data manager, yet all the standard tools are executing correctly and don't seem to be having any issues. If anyone can offer some insight or suggestions for resolving this issue, I'd be most appreciative. Best regards, -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu <http://crc.nd.edu/> ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- The information contained in this e-mail message or any attachment(s) may be confidential and/or privileged and is intended for use only by the individual(s) to whom this message is addressed. If you are not the intended recipient, any dissemination, distribution, copying, or use is strictly prohibited. If you receive this e-mail message in error, please e-mail the sender at wholtz@lygos.com <mailto:wholtz@lygos.com> and destroy this message and remove the transmission from all computer directories (including e-mail servers). Please consider the environment before printing this email. -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu <http://crc.nd.edu/>-- The information contained in this e-mail message or any attachment(s) may be confidential and/or privileged and is intended for use only by the individual(s) to whom this message is addressed. If you are not the intended recipient, any dissemination, distribution, copying, or use is strictly prohibited. If you receive this e-mail message in error, please e-mail the sender at wholtz@lygos.com mailto:wholtz@lygos.com and destroy this message and remove the transmission from all computer directories (including e-mail servers).
Please consider the environment before printing this email.
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
galaxy-dev@lists.galaxyproject.org
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Dave Bouvier -
Scott Szakonyi -
Will Holtz